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| == Overview ==
| | This page is no longer maintained. |
| The joinerCheck program is run bi-monthly on all active databases on the hgwbeta machine. Errors that are found may be newly introduced or pre-existing. Corrections to data and/or all.joiner rules that impact browser users are given priority; corrections to known errors are made as time permits.
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| * When/Who: Run bi-monthly by a member of QA
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| * Why: Catch global rule problems with all.joiner or new data problems within assemblies
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| * Where: hgwbeta:/hive/groups/qa/joinerCheck
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| * Remember: Before starting, be sure to update your source tree so that you have the latest version of all.joiner
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| == Run joinerCheck -keys ==
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| * Create new directory at: /hive/groups/qa/joinerCheck/keys/YYYYMM
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| * In the past it has been useful to run against all DBs in three batches: (1) human, (2) mouse and rat, and (3) the rest. One batch per day, for three days in a row
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| * The goal is to have each DB run without conflicting with genbank updates. Never run overnight on a Sunday (EST updates). In the past, running Mon-Tue-Wed has been successful, starting in the morning after the previous night's genbank update has finished (~8am) and ending the batch before the next night's genbank updates start (~12pm)
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| * Execute Keys program hgwbeta:/hive/groups/qa/joinerCheck/keys/YYYYMM> nice nohup joinerBatchKeys.csh [hg | mm_rn | other | extra] &
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| * When the script finished, it sends an email to whoever ran it.
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| * When complete, execute Error program> getJoinerKeyErrors.pl /hive/groups/qa/joinerCheck/keys/YYYYMM
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| == Evaluate -keys result ==
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| * Create working directory to investigate problems at: /hive/groups/qa/joinerCheck/rules/YYYYMM
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| * Review results of getJoinerKeyErrors.pl summary report
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| * Compare to the last results to find out what is known, what is new, and what has been fixed since the last run
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| * Analysis hints:
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| ** Review makedocs and all.joiner for tracks/assemblies with issues
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| ** Attempt to isolate exact problem. Is it data or a rule problem?
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| ** Original developer can help confirm track problems
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| ** If it is a genbank table, confirm that genbank updates are on then contact Mark Diekhans
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| ** Data fixes can often be made by QA, rule fixes are usually made by a developer
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| == Run joinerCheck -times ==
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| * Create new directory at: /hive/groups/qa/joinerCheck/times/YYYYMM
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| * Execute Times program hgwbeta:/hive/groups/qa/joinerCheck/keys/YYYYMM> nice nohup joinerBatchTimes.csh [hg | mm_rn | other | extra] &
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| == Evaluate -times result ==
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| * Use -keys working directory to investigate problems at: /hive/groups/qa/joinerCheck/rules/YYYYMM
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| * Review results
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| * Compare to the last results to find out what is known, what is new, and what has been fixed since the last run
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| * Analysis hints:
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| ** Any and all output is considered an error
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| ** Priority of found errors can be high if they involve proteome/known genes data
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| ** Makedoc notes are the primary source for tracking changes
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| ** Analysis hints from -keys analysis can be helpful for isolating root cause of -times errors, too
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